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Mandáková T, Krumpolcová A, Matyášek R, Volkov R, Lysak MA, Kovařík A. Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38838061 DOI: 10.1111/tpj.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address this gap in knowledge, we analyzed the 5S and 35S rDNA expression in Cardamine (Brassicaceae) allopolyploids, namely C. × insueta (2n = 3x = 24, genome composition RRA), C. flexuosa (2n = 4x = 32, AAHH), and C. scutata (2n = 4x = 32, PPAA) which share a common diploid ancestor (AA). We employed high-throughput sequencing of transcriptomes and genomes and phylogenetic analyses of 5S rRNA variants. The genomic organization of rDNA was further scrutinized through clustering and fluorescence in situ hybridization. In the C. × insueta allotriploid, we observed uniparental dominant expression of 5S and 35S rDNA loci. In the C. flexuosa and C. scutata allotetraploids, the expression pattern differed, with the 35S rDNA being expressed from the A subgenome, whereas the 5S rDNA was expressed from the partner subgenome. Both C. flexuosa and C. scutata but not C. × insueta showed copy and locus number changes. We conclude that in stabilized allopolyploids, transcription of ribosomal RNA components occurs from different subgenomes. This phenomenon appears to result in the formation of chimeric ribosomes comprising rRNA molecules derived from distinct parental origins. We speculate that the interplay of epigenetic silencing and rDNA rearrangements introduces an additional layer of variation in multimolecule ribosomal complexes, potentially contributing to the evolutionary success of allopolyploids.
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Affiliation(s)
- Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Alice Krumpolcová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
| | - Roman Matyášek
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
| | - Roman Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, 58012, Chernivtsi, Ukraine
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Ales Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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3
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Burenkova OV, Grigorenko EL. The role of epigenetic mechanisms in the long-term effects of early-life adversity and mother-infant relationship on physiology and behavior of offspring in laboratory rats and mice. Dev Psychobiol 2024; 66:e22479. [PMID: 38470450 PMCID: PMC10959231 DOI: 10.1002/dev.22479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024]
Abstract
Maternal care during the early postnatal period of altricial mammals is a key factor in the survival and adaptation of offspring to environmental conditions. Natural variations in maternal care and experimental manipulations with maternal-child relationships modeling early-life adversity (ELA) in laboratory rats and mice have a strong long-term influence on the physiology and behavior of offspring in rats and mice. This literature review is devoted to the latest research on the role of epigenetic mechanisms in these effects of ELA and mother-infant relationship, with a focus on the regulation of hypothalamic-pituitary-adrenal axis and brain-derived neurotrophic factor. An important part of this review is dedicated to pharmacological interventions and epigenetic editing as tools for studying the causal role of epigenetic mechanisms in the development of physiological and behavioral profiles. A special section of the manuscript will discuss the translational potential of the discussed research.
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Affiliation(s)
- Olga V. Burenkova
- Department of Psychology, University of Houston, Houston, Texas, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, Texas, USA
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, Texas, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, Texas, USA
- Center for Cognitive Sciences, Sirius University of Science and Technology, Sochi, Russia
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Child Study Center, Yale University, New Haven, Connecticut, USA
- Research Administration, Moscow State University for Psychology and Education, Moscow, Russia
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4
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He Q, Fan X, Wang S, Chen S, Chen J. Juvenile hormone inhibits adult cuticle formation in Drosophila melanogaster through Kr-h1/Dnmt2-mediated DNA methylation of Acp65A promoter. INSECT MOLECULAR BIOLOGY 2024; 33:124-135. [PMID: 37916965 DOI: 10.1111/imb.12884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023]
Abstract
Differentiation of imaginal epidermal cells of Drosophila melanogaster to form adult cuticles occurs at approximately 40-93 h after puparium formation. Juvenile hormone (JH) given at pupariation results in formation of a second pupal cuticle in the abdomen instead of the adult cuticle. Although the adult cuticle gene Acp65A has been reported to be down-regulated following JH treatment, the regulatory mechanism remains unclear. Here, we found that the JH primary response gene Krüppel homologue 1 (Kr-h1) plays a vital role in the repression of adult cuticle formation through the mediation of JH action. Overexpression of Kr-h1 mimicked-while knocking down of Kr-h1 attenuated-the inhibitory action of JH on the formation of the adult abdominal cuticle. Further, we found that Kr-h1 inhibited the transcription of Acp65A by directly binding to the consensus Kr-h1 binding site (KBS) within the Acp65A promoter region. Moreover, the DNA methyltransferase Dnmt2 was shown to interact with Kr-h1, combined with the KBS to promote the DNA methylation of sequences around the KBS, in turn inhibiting the transcription of Acp65A. This study advances our understanding of the molecular basis of the "status quo" action of JH on the Drosophila adult metamorphosis.
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Affiliation(s)
- Qianyu He
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaochun Fan
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shunxin Wang
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shanshan Chen
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jinxia Chen
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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Hao Q, Liu M, Daulatabad SV, Gaffari S, Song YJ, Srivastava R, Bhaskar S, Moitra A, Mangan H, Tseng E, Gilmore RB, Frier SM, Chen X, Wang C, Huang S, Chamberlain S, Jin H, Korlach J, McStay B, Sinha S, Janga SC, Prasanth SG, Prasanth KV. Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression. eLife 2024; 13:e80684. [PMID: 38240312 PMCID: PMC10852677 DOI: 10.7554/elife.80684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Out of the several hundred copies of rRNA genes arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, ~50% remain transcriptionally inactive. NOR-associated sequences and epigenetic modifications contribute to the differential expression of rRNAs. However, the mechanism(s) controlling the dosage of active versus inactive rRNA genes within each NOR in mammals is yet to be determined. We have discovered a family of ncRNAs, SNULs (Single NUcleolus Localized RNA), which form constrained sub-nucleolar territories on individual NORs and influence rRNA expression. Individual members of the SNULs monoallelically associate with specific NOR-containing chromosomes. SNULs share sequence similarity to pre-rRNA and localize in the sub-nucleolar compartment with pre-rRNA. Finally, SNULs control rRNA expression by influencing pre-rRNA sorting to the DFC compartment and pre-rRNA processing. Our study discovered a novel class of ncRNAs influencing rRNA expression by forming constrained nucleolar territories on individual NORs.
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Affiliation(s)
- Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Minxue Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Saba Gaffari
- Department of Computer Science, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Shivang Bhaskar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Anurupa Moitra
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | | | - Rachel B Gilmore
- Department of Genetics and Genome Sciences, University of Connecticut School of MedicineFarmingtonUnited States
| | | | - Xin Chen
- Department of Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Chengliang Wang
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern UniversityChicagoUnited States
| | - Stormy Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of MedicineFarmingtonUnited States
| | - Hong Jin
- Department of Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | | | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Department of Biomedical Engineering, Georgia TechAtlantaUnited States
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Cancer Center at Illinois, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Cancer Center at Illinois, University of Illinois at Urbana-ChampaignUrbanaUnited States
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Priyadarshini N, Venkatarama Puppala N, Jayaprakash JP, Khandelia P, Sharma V, Mohannath G. Downregulation of ribosomal RNA (rRNA) genes in human head and neck squamous cell carcinoma (HNSCC) cells correlates with rDNA promoter hypermethylation. Gene 2023; 888:147793. [PMID: 37696422 DOI: 10.1016/j.gene.2023.147793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Eukaryotes carry hundreds of ribosomal RNA (rRNA) genes as tandem arrays, which generate rRNA for protein synthesis. Humans carry ∼ 400 rRNA gene copies and their expression is epigenetically regulated. Dysregulation of rRNA synthesis and ribosome biogenesis are characteristic features of cancers. Targeting aberrant rRNA expression for cancer therapy is being explored. Head and neck squamous cell carcinoma (HNSCC) is among the most prevalent cancers globally. Using quantitative PCR and bisulfite sequencing, we show that rRNA genes are downregulated and their promoters are hypermethylated in HNSCC cell lines. These findings may have relevance for prognosis and diagnosis of HNSCC.
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Affiliation(s)
- Neha Priyadarshini
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Navinchandra Venkatarama Puppala
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Jayasree Peroth Jayaprakash
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, Telangana, India.
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9
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Pírek P, Kryštofová K, Kováčová I, Kromerová A, Zachová D, Helia O, Panzarová K, Fajkus J, Zdráhal Z, Lochmanová G, Fojtová M. Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors. PLANTS (BASEL, SWITZERLAND) 2023; 12:4177. [PMID: 38140504 PMCID: PMC10747063 DOI: 10.3390/plants12244177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli.
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Affiliation(s)
- Pavlína Pírek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Karolína Kryštofová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Ingrid Kováčová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Anna Kromerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Klára Panzarová
- PSI (Photon Systems Instruments), spol. s.r.o., 66424 Drásov, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
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10
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Ando S, Nomoto M, Iwakawa H, Vial-Pradel S, Luo L, Sasabe M, Ohbayashi I, Yamamoto KT, Tada Y, Sugiyama M, Machida Y, Kojima S, Machida C. Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3621. [PMID: 37896084 PMCID: PMC10610122 DOI: 10.3390/plants12203621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.
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Affiliation(s)
- Sayuri Ando
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Michiko Sasabe
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, Hirosaki 036-8561, Japan;
| | - Iwai Ohbayashi
- Department of Life Sciences, National Cheng Kung University, Tainan City 701, Taiwan;
| | - Kotaro T. Yamamoto
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Munetaka Sugiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Yasunori Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
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11
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Huang Y, Liu Y, Guo X, Fan C, Yi C, Shi Q, Su H, Liu C, Yuan J, Liu D, Yang W, Han F. New insights on the evolution of nucleolar dominance in newly resynthesized hexaploid wheat Triticum zhukovskyi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1298-1315. [PMID: 37246611 DOI: 10.1111/tpj.16320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Nucleolar dominance (ND) is a widespread epigenetic phenomenon in hybridizations where nucleolus transcription fails at the nucleolus organizer region (NOR). However, the dynamics of NORs during the formation of Triticum zhukovskyi (GGAu Au Am Am ), another evolutionary branch of allohexaploid wheat, remains poorly understood. Here, we elucidated genetic and epigenetic changes occurring at the NOR loci within the Am , G, and D subgenomes during allopolyploidization by synthesizing hexaploid wheat GGAu Au Am Am and GGAu Au DD. In T. zhukovskyi, Au genome NORs from T. timopheevii (GGAu Au ) were lost, while the second incoming NORs from T. monococcum (Am Am ) were retained. Analysis of the synthesized T. zhukovskyi revealed that rRNA genes from the Am genome were silenced in F1 hybrids (GAu Am ) and remained inactive after genome doubling and subsequent self-pollinations. We observed increased DNA methylation accompanying the inactivation of NORs in the Am genome and found that silencing of NORs in the S1 generation could be reversed by a cytidine methylase inhibitor. Our findings provide insights into the ND process during the evolutionary period of T. zhukovskyi and highlight that inactive rDNA units may serve as a 'first reserve' in the form of R-loops, contributing to the successful evolution of T. zhukovskyi.
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Affiliation(s)
- Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Handong Su
- Huazhong Agricultural University, Hubei, 430070, China
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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12
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Pikaard CS, Chandrasekhara C, McKinlay A, Enganti R, Fultz D. Reaching for the off switch in nucleolar dominance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1185-1192. [PMID: 37228042 PMCID: PMC10524600 DOI: 10.1111/tpj.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023]
Abstract
Nucleolus organizer regions (NORs) are eukaryotic chromosomal loci where ribosomal RNA (rRNA) genes are clustered, typically in hundreds to thousands of copies. Transcription of these rRNA genes by RNA polymerase I and processing of their transcripts results in the formation of the nucleolus, the sub-nuclear domain in which ribosomes are assembled. Approximately 90 years ago, cytogenetic observations revealed that NORs inherited from the different parents of an interspecific hybrid sometimes differ in morphology at metaphase. Fifty years ago, those chromosomal differences were found to correlate with differences in rRNA gene transcription and the phenomenon became known as nucleolar dominance. Studies of the past 30 years have revealed that nucleolar dominance results from selective rRNA gene silencing, involving repressive chromatin modifications, and occurs in pure species as well as hybrids. Recent evidence also indicates that silencing depends on the NOR in which an rRNA gene is located, and not on the gene's sequence. In this perspective, we discuss how our thinking about nucleolar dominance has shifted over time from the kilobase scale of individual genes to the megabase scale of NORs and chromosomes and questions that remain unanswered in the search for a genetic and biochemical understanding of the off switch.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Chinmayi Chandrasekhara
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Anastasia McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Ramya Enganti
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Dalen Fultz
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
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13
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Borowska-Zuchowska N, Mykhailyk S, Robaszkiewicz E, Matysiak N, Mielanczyk L, Wojnicz R, Kovarik A, Hasterok R. Switch them off or not: selective rRNA gene repression in grasses. TRENDS IN PLANT SCIENCE 2023; 28:661-672. [PMID: 36764871 DOI: 10.1016/j.tplants.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/11/2023] [Indexed: 05/13/2023]
Abstract
Nucleolar dominance (ND) is selective epigenetic silencing of 35-48S rDNA loci. In allopolyploids, it is frequently manifested at the cytogenetic level by the inactivation of nucleolar organiser region(s) (NORs) inherited from one or several evolutionary ancestors. Grasses are ecologically and economically one of the most important land plant groups, which have frequently evolved through hybridisation and polyploidisation events. Here we review common and unique features of ND phenomena in this monocot family from cytogenetic, molecular, and genomic perspectives. We highlight recent advances achieved by using an allotetraploid model grass, Brachypodium hybridum, where ND commonly occurs at a population level, and we cover modern genomic approaches that decipher structural features of core arrays of NORs.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
| | - Serhii Mykhailyk
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Natalia Matysiak
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland
| | - Lukasz Mielanczyk
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland; Silesian Nanomicroscopy Centre in Zabrze, Silesia LabMed - Research and Implementation Centre, Medical University of Silesia, Katowice, Poland
| | - Romuald Wojnicz
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland; Silesian Nanomicroscopy Centre in Zabrze, Silesia LabMed - Research and Implementation Centre, Medical University of Silesia, Katowice, Poland
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, CZ-61200 Brno, Czech Republic
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
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14
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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15
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Zhang Z, Yang W, Chu Y, Yin X, Liang Y, Wang Q, Wang L, Han Z. AtHD2D, a plant-specific histone deacetylase involved in abscisic acid response and lateral root development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7380-7400. [PMID: 36125085 DOI: 10.1093/jxb/erac381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
In eukaryotes, histone acetylation levels directly regulate downstream gene expression. As a plant-specific histone deacetylase (HDAC), HD2D is involved in plant development and abiotic stress. However, the response of HD2D to drought stress and its interacting proteins, is still unclear. In this study, we analysed HD2D gene expression patterns in Arabidopsis, revealing that HD2D gene was highly expressed in roots and rosette leaves, but poorly expressed in other tissues such as stems, flowers, and young siliques. The HD2D gene expression was induced by d-mannitol. We investigated the responses to drought stress in the wild-type plant, HD2D overexpression lines, and hd2d mutants. HD2D-overexpressing lines showed abscisic acid (ABA) hypersensitivity and drought tolerance, and these phenotypes were not present in hd2d mutants. RNA-seq analysis revealed the transcriptome changes caused by HD2D under drought stress, and showed that HD2D responded to drought stress via the ABA signalling pathway. In addition, we demonstrated that CASEIN KINASE II (CKA4) directly interacted with HD2D. The phosphorylation of Ser residues on HD2D by CKA4 enhanced HD2D enzymatic activity. Furthermore, the phosphorylation of HD2D was shown to contribute to lateral root development and ABA sensing in Arabidopsis, but, these phenotypes could not be reproduced by the overexpression of Ser-phospho-null HD2D lines. Collectively, this study suggests that HD2D responded to drought stress by regulating the ABA signalling pathway, and the expression of drought stress-related genes. The regulatory mechanism of HD2D mediated by CKII phosphorylation provides new insights into the ABA response and lateral root development in Arabidopsis.
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Affiliation(s)
- Zhaochen Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Weixia Yang
- College of Chemistry & Pharmacy, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueqi Liang
- College of Innovation and Experiment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Qiuping Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Lei Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
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16
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Asim MN, Ibrahim MA, Malik MI, Razzak I, Dengel A, Ahmed S. Histone-Net: a multi-paradigm computational framework for histone occupancy and modification prediction. COMPLEX INTELL SYST 2022. [DOI: 10.1007/s40747-022-00802-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractDeep exploration of histone occupancy and covalent post-translational modifications (e.g., acetylation, methylation) is essential to decode gene expression regulation, chromosome packaging, DNA damage, and transcriptional activation. Existing computational approaches are unable to precisely predict histone occupancy and modifications mainly due to the use of sub-optimal statistical representation of histone sequences. For the establishment of an improved histone occupancy and modification landscape for multiple histone markers, the paper in hand presents an end-to-end computational multi-paradigm framework “Histone-Net”. To learn local and global residue context aware sequence representation, Histone-Net generates unsupervised higher order residue embeddings (DNA2Vec) and presents a different application of language modelling, where it encapsulates histone occupancy and modification information while generating higher order residue embeddings (SuperDNA2Vec) in a supervised manner. We perform an intrinsic and extrinsic evaluation of both presented distributed representation learning schemes. A comprehensive empirical evaluation of Histone-Net over ten benchmark histone markers data sets for three different histone sequence analysis tasks indicates that SuperDNA2Vec sequence representation and softmax classifier-based approach outperforms state-of-the-art approach by an average accuracy of 7%. To eliminate the overhead of training separate binary classifiers for all ten histone markers, Histone-Net is evaluated in multi-label classification paradigm, where it produces decent performance for simultaneous prediction of histone occupancy, acetylation, and methylation.
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17
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Unraveling the DNA Methylation in the rDNA Foci in Mutagen-Induced Brachypodium distachyon Micronuclei. Int J Mol Sci 2022; 23:ijms23126797. [PMID: 35743241 PMCID: PMC9224279 DOI: 10.3390/ijms23126797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
Many years have passed since micronuclei were first observed then accepted as an indicator of the effect of mutagens. However, the possible mechanisms of their formation and elimination from the cell are still not fully understood. Various stresses, including mutagens, can alter gene expression through changes in DNA methylation in plants. In this study we demonstrate for the first time DNA methylation in the foci of 5S and 35S rDNA sequences in individual Brachypodium distachyon micronuclei that are induced by mutagenic treatment with maleic acid hydrazide (MH). The impact of MH on global epigenetic modifications in nuclei and micronuclei has been studied in plants before; however, no in situ analyses of DNA methylation in specific DNA sequence sites are known. To address this problem, we used sequential immunodetection of 5-methylcytosine and fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes on the non-dividing cells of B. distachyon. Such investigations into the presence or absence of DNA methylation within specific DNA sequences are extremely important in plant mutagenesis in the light of altering gene expression.
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18
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Ullah I, Ansari HA, Verry IM, Hussain SW, Ellison NW, McManus MT, Williams WM. Introgression of Trifolium ambiguum Into Allotetraploid White Clover ( Trifolium repens) Using the Ancestral Parent Trifolium occidentale as a Bridging Species. FRONTIERS IN PLANT SCIENCE 2022; 13:858714. [PMID: 35371143 PMCID: PMC8971954 DOI: 10.3389/fpls.2022.858714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
White clover (Trifolium repens) is an allotetraploid pasture legume widely used in moist temperate climates, but its vulnerability to drought, grazing pressure and pests has restricted its wider use. A related species, Caucasian clover (Trifolium ambiguum), is a potential source of resistances to drought, cold, grazing pressure and pests that could potentially be transferred to white clover by interspecific hybridization. Although direct hybridization has been achieved with difficulty, the hybrids have not been easy to backcross for introgression breeding and no interspecific chromosome recombination has been demonstrated. The present work shows that interspecific recombination can be achieved by using Trifolium occidentale, one of the ancestral parents of T. repens, as a bridging species and that large white clover breeding populations carrying recombinant chromosomes can be generated. A 4x hybrid between T. ambiguum and T. occidentale was crossed with T. repens and then backcrossed for two generations. Five backcross hybrid plants with phenotypes appearing to combine traits from the parent species were selected for FISH-GISH analyses. Recombinant chromosome segments from T. ambiguum were found in all five plants, suggesting that recombination frequencies were significant and sufficient for introgression breeding. Despite early chromosome imbalances, the backcross populations were fertile and produced large numbers of seeds. These hybrids represent a major new resource for the breeding of novel resilient forms of white clover.
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Affiliation(s)
- Ihsan Ullah
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
- College of Sciences, Massey University, Palmerston North, New Zealand
| | - Helal A. Ansari
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
| | - Isabelle M. Verry
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
| | | | - Nick W. Ellison
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
| | | | - Warren M. Williams
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
- College of Sciences, Massey University, Palmerston North, New Zealand
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19
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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20
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Hemleben V, Grierson D, Borisjuk N, Volkov RA, Kovarik A. Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:797348. [PMID: 34992624 PMCID: PMC8724763 DOI: 10.3389/fpls.2021.797348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss - from a personal view - the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on "Molecular organization, evolution, and function of ribosomal DNA."
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Affiliation(s)
- Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Donald Grierson
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nikolai Borisjuk
- School of Life Sciences, Huaiyin Normal University, Huai'an, China
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Ales Kovarik
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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21
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Asadi MR, Hassani M, Kiani S, Sabaie H, Moslehian MS, Kazemi M, Ghafouri-Fard S, Taheri M, Rezazadeh M. The Perspective of Dysregulated LncRNAs in Alzheimer's Disease: A Systematic Scoping Review. Front Aging Neurosci 2021; 13:709568. [PMID: 34621163 PMCID: PMC8490871 DOI: 10.3389/fnagi.2021.709568] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
LncRNAs act as part of non-coding RNAs at high levels of complex and stimulatory configurations in basic molecular mechanisms. Their extensive regulatory activity in the CNS continues on a small scale, from the functions of synapses to large-scale neurodevelopment and cognitive functions, aging, and can be seen in both health and disease situations. One of the vast consequences of the pathological role of dysregulated lncRNAs in the CNS due to their role in a network of regulatory pathways can be manifested in Alzheimer's as a neurodegenerative disease. The disease is characterized by two main hallmarks: amyloid plaques due to the accumulation of β-amyloid components and neurofibrillary tangles (NFT) resulting from the accumulation of phosphorylated tau. Numerous studies in humans, animal models, and various cell lines have revealed the role of lncRNAs in the pathogenesis of Alzheimer's disease. This scoping review was performed with a six-step strategy and based on the Prisma guideline by systematically searching the publications of seven databases. Out of 1,591 records, 69 articles were utterly aligned with the specified inclusion criteria and were summarized in the relevant table. Most of the studies were devoted to BACE1-AS, NEAT1, MALAT1, and SNHG1 lncRNAs, respectively, and about one-third of the studies investigated a unique lncRNA. About 56% of the studies reported up-regulation, and 7% reported down-regulation of lncRNAs expressions. Overall, this study was conducted to investigate the association between lncRNAs and Alzheimer's disease to make a reputable source for further studies and find more molecular therapeutic goals for this disease.
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Affiliation(s)
- Mohammad Reza Asadi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Hassani
- Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shiva Kiani
- Department of Molecular Genetics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Sadat Moslehian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Kazemi
- Department of Social Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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22
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Jiang X, Song Q, Ye W, Chen ZJ. Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. Nat Ecol Evol 2021; 5:1382-1393. [PMID: 34413505 PMCID: PMC8484014 DOI: 10.1038/s41559-021-01523-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023]
Abstract
During evolution successful allopolyploids must overcome 'genome shock' between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsis thaliana (TT) and Arabidopsis arenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.
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Affiliation(s)
- Xinyu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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23
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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24
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Rausch C, Zhang P, Casas-Delucchi CS, Daiß JL, Engel C, Coster G, Hastert FD, Weber P, Cardoso MC. Cytosine base modifications regulate DNA duplex stability and metabolism. Nucleic Acids Res 2021; 49:12870-12894. [PMID: 34133727 PMCID: PMC8682791 DOI: 10.1093/nar/gkab509] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
DNA base modifications diversify the genome and are essential players in development. Yet, their influence on DNA physical properties and the ensuing effects on genome metabolism are poorly understood. Here, we focus on the interplay of cytosine modifications and DNA processes. We show by a combination of in vitro reactions with well-defined protein compositions and conditions, and in vivo experiments within the complex networks of the cell that cytosine methylation stabilizes the DNA helix, increasing its melting temperature and reducing DNA helicase and RNA/DNA polymerase speed. Oxidation of methylated cytosine, however, reverts the duplex stabilizing and genome metabolic effects to the level of unmodified cytosine. We detect this effect with DNA replication and transcription proteins originating from different species, ranging from prokaryotic and viral to the eukaryotic yeast and mammalian proteins. Accordingly, lack of cytosine methylation increases replication fork speed by enhancing DNA helicase unwinding speed in cells. We further validate that this cannot simply be explained by altered global DNA decondensation, changes in histone marks or chromatin structure and accessibility. We propose that the variegated deposition of cytosine modifications along the genome regulates DNA helix stability, thereby providing an elementary mechanism for local fine-tuning of DNA metabolism.
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Affiliation(s)
- Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Center for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, Guizhou 550004, China
| | | | - Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gideon Coster
- Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, UK
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Patrick Weber
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
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25
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Lopez FB, Fort A, Tadini L, Probst AV, McHale M, Friel J, Ryder P, Pontvianne F, Pesaresi P, Sulpice R, McKeown P, Brychkova G, Spillane C. Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number. THE PLANT CELL 2021; 33:1135-1150. [PMID: 33793816 PMCID: PMC8225240 DOI: 10.1093/plcell/koab020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/24/2020] [Indexed: 05/08/2023]
Abstract
The 45S rRNA genes (rDNA) are among the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as 'back-up' copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte, we reduced 45S rDNA copy number (CN) to a plateau of ∼10%. Two independent lines had rDNA CNs reduced by up to 90% at the T7 generation, named low copy number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates, and steady-state levels remained the same as wild-type plants. Gene dosage compensation of rRNA transcript levels was associated with reduction of silencing histone marks at rDNA loci and altered Nucleolar Organiser Region 2 organization. Although overall genome integrity of LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines. Transcriptome analysis of LCN seedlings identified several shared dysregulated genes and pathways in both independent lines. Cas9 genome editing of rRNA repeats to generate LCN lines provides a powerful technique to elucidate rDNA dosage compensation mechanisms and impacts of low rDNA CN on genome stability, development, and cellular processes.
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Affiliation(s)
- Francesca B Lopez
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Luca Tadini
- Dipartimento di Bioscienze, Universit� degli Studi di Milano, 20133 Milano, Italy
| | - Aline V Probst
- CNRS, GReD, Universit� Clermont Auvergne, INSERM, 63001 Clermont–Ferrand, France
| | - Marcus McHale
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - James Friel
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Fr�d�ric Pontvianne
- CNRS, Laboratoire G�nome et D�veloppement des Plantes (LGDP), Universit� de Perpignan Via Domitia, Perpignan, France
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Universit� degli Studi di Milano, 20133 Milano, Italy
| | - Ronan Sulpice
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter McKeown
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Author for correspondence:
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26
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Liu Y, Yuan J, Jia G, Ye W, Jeffrey Chen Z, Song Q. Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:678-690. [PMID: 33131144 DOI: 10.1111/tpj.15063] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 05/02/2023]
Abstract
Bread wheat (Triticum aestivum) is an allohexaploid that was formed via two allopolyploidization events. Growing evidence suggests histone modifications are involved in the response to 'genomic shock' and environmental adaptation during polyploid formation and evolution. However, the role of histone modifications, especially histone H3 lysine-27 dimethylation (H3K27me2), in genome evolution remains elusive. Here we analyzed H3K27me2 and H3K27me3 profiles in hexaploid wheat and its tetraploid and diploid relatives. Although H3K27me3 levels were relatively stable among wheat species with different ploidy levels, H3K27me2 intensities increased concurrent with increased ploidy levels, and H3K27me2 peaks were colocalized with massively amplified DTC transposons (CACTA family) in euchromatin, which may silence euchromatic transposons to maintain genome stability during polyploid wheat evolution. Consistently, the distribution of H3K27me2 is mutually exclusive with another repressive histone mark, H3K9me2, that mainly silences transposons in heterochromatic regions. Remarkably, the regions with low H3K27me2 levels (named H3K27me2 valleys) were associated with the formation of DNA double-strand breaks in genomes of wheat, maize (Zea mays) and Arabidopsis. Our results provide a comprehensive view of H3K27me2 and H3K27me3 distributions during wheat evolution, which support roles for H3K27me2 in silencing euchromatic transposons to maintain genome stability and in modifying genetic recombination landscapes. These genomic insights may empower breeding improvement of crops.
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Affiliation(s)
- Yanfeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Guanghong Jia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
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27
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Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids. Genes (Basel) 2021; 12:genes12010082. [PMID: 33440604 PMCID: PMC7827416 DOI: 10.3390/genes12010082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.
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28
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Ramos LF, Silva CM, Pansa CC, Moraes KCM. Non-alcoholic fatty liver disease: molecular and cellular interplays of the lipid metabolism in a steatotic liver. Expert Rev Gastroenterol Hepatol 2021; 15:25-40. [PMID: 32892668 DOI: 10.1080/17474124.2020.1820321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Non-alcoholic fatty liver disease (NAFLD) affects ~25% of world population and cases have increased in recent decades. These anomalies have several etiologies; however, obesity and metabolic dysfunctions are the most relevant causes. Despite being considered a public health problem, no effective therapeutic approach to treat NAFLD is available. For that, a deep understanding of metabolic routes that support hepatic diseases is needed. AREAS COVERED This review covers aspects of the onset of NAFLD. Thereby, biochemistry routes as well as cellular and metabolic effects of the gut microbiota in body's homeostasis and epigenetics are contextualized. EXPERT OPINION Recently, the development of biological sciences has generated innovative knowledge, bringing new insights and perspectives to clarify the systems biology of liver diseases. A detailed comprehension of epigenetics mechanisms will offer possibilities to develop new therapeutic and diagnostic strategies for NAFLD. Different epigenetic processes have been reported that are modulated by the environment such as gut microbiota, suggesting strong interplays between cellular behavior and pathology. Thus, a more complete description of such mechanisms in hepatic diseases will help to clarify how to control the establishment of fatty liver, and precisely describe molecular interplays that potentially control NAFLD.
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Affiliation(s)
- Letícia F Ramos
- Molecular Biology Laboratory, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista "Júlio de Mesquita Filho" - Campus Rio Claro, Instituto de Biociências , Rio Claro, Brazil
| | - Caio M Silva
- Molecular Biology Laboratory, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista "Júlio de Mesquita Filho" - Campus Rio Claro, Instituto de Biociências , Rio Claro, Brazil
| | - Camila C Pansa
- Molecular Biology Laboratory, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista "Júlio de Mesquita Filho" - Campus Rio Claro, Instituto de Biociências , Rio Claro, Brazil
| | - Karen C M Moraes
- Molecular Biology Laboratory, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista "Júlio de Mesquita Filho" - Campus Rio Claro, Instituto de Biociências , Rio Claro, Brazil
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29
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Borowska-Zuchowska N, Robaszkiewicz E, Mykhailyk S, Wartini J, Pinski A, Kovarik A, Hasterok R. To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum. FRONTIERS IN PLANT SCIENCE 2021; 12:768347. [PMID: 34938308 PMCID: PMC8685274 DOI: 10.3389/fpls.2021.768347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/09/2021] [Indexed: 05/20/2023]
Abstract
Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root, leaf, and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- *Correspondence: Natalia Borowska-Zuchowska,
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Serhii Mykhailyk
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Wartini
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Artur Pinski
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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30
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Tapia-Pastrana F. Differential Amphiplasty and Nucleolar Dominance in Somatic Metaphase Cells as Evidence of Hybridization in Prosopis juliflora (Leguminosae, Mimosoideae). CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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The Role of Histone Acetylation-/Methylation-Mediated Apoptotic Gene Regulation in Hepatocellular Carcinoma. Int J Mol Sci 2020; 21:ijms21238894. [PMID: 33255318 PMCID: PMC7727670 DOI: 10.3390/ijms21238894] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/31/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Epigenetics, an inheritable phenomenon, which influences the expression of gene without altering the DNA sequence, offers a new perspective on the pathogenesis of hepatocellular carcinoma (HCC). Nonalcoholic steatohepatitis (NASH) is projected to account for a significant share of HCC incidence due to the growing prevalence of various metabolic disorders. One of the major molecular mechanisms involved in epigenetic regulation, post-translational histone modification seems to coordinate various aspects of NASH which will further progress to HCC. Mounting evidence suggests that the orchestrated events of cellular and nuclear changes during apoptosis can be regulated by histone modifications. This review focuses on the current advances in the study of acetylation-/methylation-mediated histone modification in apoptosis and the implication of these epigenetic regulations in HCC. The reversibility of epigenetic alterations and the agents that can target these alterations offers novel therapeutic approaches and strategies for drug development. Further molecular mechanistic studies are required to enhance information governing these epigenetic modulators, which will facilitate the design of more effective diagnosis and treatment options.
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32
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Lee MH, Lee J, Choi SH, Jie EY, Jeong JC, Kim CY, Kim SW. The Effect of Sodium Butyrate on Adventitious Shoot Formation Varies among the Plant Species and the Explant Types. Int J Mol Sci 2020; 21:E8451. [PMID: 33182800 PMCID: PMC7696800 DOI: 10.3390/ijms21228451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/24/2022] Open
Abstract
Histone acetylation plays an important role in plant growth and development. Here, we investigated the effect of sodium butyrate (NaB), a histone deacetylase inhibitor, on adventitious shoot formation from protoplast-derived calli and cotyledon explants of tobacco (Nicotiana benthamiana) and tomato (Solanum lycopersicum). The frequency of adventitious shoot formation from protoplast-derived calli was higher in shoot induction medium (SIM) containing NaB than in the control. However, the frequency of adventitious shoot formation from cotyledon explants of tobacco under the 0.1 mM NaB treatment was similar to that in the control, but it decreased with increasing NaB concentration. Unlike in tobacco, NaB decreased adventitious shoot formation in tomato explants in a concentration-dependent manner, but it did not have any effect on adventitious shoot formation in calli. NaB inhibited or delayed the expression of D-type cyclin (CYCD3-1) and shoot-regeneration regulatory gene WUSCHEL (WUS) in cotyledon explants of tobacco and tomato. However, compared to that in control SIM, the expression of WUS was promoted more rapidly in tobacco calli cultured in NaB-containing SIM, but the expression of CYCD3-1 was inhibited. In conclusion, the effect of NaB on adventitious shoot formation and expression of CYCD3-1 and WUS genes depended on the plant species and whether the effects were tested on explants or protoplast-derived calli.
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Affiliation(s)
| | | | | | | | | | | | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (M.H.L.); (J.L.); (S.H.C.); (E.Y.J.); (J.C.J.); (C.Y.K.)
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Lim Y, Bak SY, Lee SH, Kim SK. Comparative Single-Molecule Kinetic Study for the Effect of Base Methylation on a Model DNA-Protein Interaction. J Phys Chem Lett 2020; 11:8048-8052. [PMID: 32885977 DOI: 10.1021/acs.jpclett.0c01929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We studied how the interaction between HindIII endonuclease and dsDNA is affected by the single-base modification of the latter by a single-molecule kinetic assay. For a comparative study of chemical modifications, we measured the binding and unbinding rates of the HindIII-DNA complex for normal dsDNA, methylated DNA, and hydroxymethylated DNA. We found that methylation of DNA at the recognition site results in a large increase in the unbinding rate due to the steric effect, which is consistent with the standard free energy change in the transition state. On the contrary, methylation minimally affects the binding rate, as simultaneous increases in the activation energy and the pre-exponential factor compensate for each other.
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Affiliation(s)
- Youngbin Lim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - So Young Bak
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sang Hak Lee
- Department of Chemistry, Pusan National University, Pusan 46241, Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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Borowska‐Zuchowska N, Kovarik A, Robaszkiewicz E, Tuna M, Tuna GS, Gordon S, Vogel JP, Hasterok R. The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1810-1825. [PMID: 32506573 PMCID: PMC7497271 DOI: 10.1111/tpj.14869] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 05/22/2023]
Abstract
Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.
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Affiliation(s)
- Natalia Borowska‐Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Ales Kovarik
- Department of Molecular EpigeneticsInstitute of BiophysicsAcademy of Sciences of the Czech Republic, v.v.i.Královopolská 135Brno612 65Czech Republic
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Metin Tuna
- Department of Field CropsFaculty of AgricultureTekirdag Namik Kemal UniversitySuleymanpasaTekirdag59030Turkey
| | | | - Sean Gordon
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
| | - John P. Vogel
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
- University CaliforniaBerkeley, BerkeleyCA94720USA
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
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Okamoto S, Negishi K, Toyama Y, Ushijima T, Morohashi K. Leaf Trichome Distribution Pattern in Arabidopsis Reveals Gene Expression Variation Associated with Environmental Adaptation. PLANTS 2020; 9:plants9070909. [PMID: 32709158 PMCID: PMC7412270 DOI: 10.3390/plants9070909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 01/28/2023]
Abstract
Gene expression varies stochastically even in both heterogenous and homogeneous cell populations. This variation is not simply useless noise; rather, it is important for many biological processes. Unicellular organisms or cultured cell lines are useful for analyzing the variation in gene expression between cells; however, owing to technical challenges, the biological relevance of this variation in multicellular organisms such as higher plants remain unclear. Here, we addressed the biological relevance of this variation between cells by examining the genetic basis of trichome distribution patterns in Arabidopsis thaliana. The distribution pattern of a trichome on a leaf is stochastic and can be mathematically represented using Turing’s reaction-diffusion (RD) model. We analyzed simulations based on the RD model and found that the variability in the trichome distribution pattern increased with the increase in stochastic variation in a particular gene expression. Moreover, differences in heat-dependent variability of the trichome distribution pattern between the accessions showed a strong correlation with environmental factors to which each accession was adapted. Taken together, we successfully visualized variations in gene expression by quantifying the variability in the Arabidopsis trichome distribution pattern. Thus, our data provide evidence for the biological importance of variations in gene expression for environmental adaptation.
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Affiliation(s)
- Shotaro Okamoto
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
| | - Kohei Negishi
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
| | - Yuko Toyama
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
| | - Takeo Ushijima
- Department of Mathematics, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan;
| | - Kengo Morohashi
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: or ; Tel.: +1-614-407-6676
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Kopka J. Systematic Review of Plant Ribosome Heterogeneity and Specialization. FRONTIERS IN PLANT SCIENCE 2020; 11:948. [PMID: 32670337 PMCID: PMC7332886 DOI: 10.3389/fpls.2020.00948] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/10/2020] [Indexed: 05/25/2023]
Abstract
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Yin-Chen Hsieh
- Bioinformatics Subdivision, Wageningen University, Wageningen, Netherlands
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
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Pagano A, L'Andolina C, Sabatini ME, de Sousa Araújo S, Balestrazzi A, Macovei A. Sodium butyrate induces genotoxic stress in function of photoperiod variations and differentially modulates the expression of genes involved in chromatin modification and DNA repair in Petunia hybrida seedlings. PLANTA 2020; 251:102. [PMID: 32350684 DOI: 10.1007/s00425-020-03392-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Sodium butyrate applied to Petunia hybrida seeds under a long-day photoperiod has a negative impact (reduced seedling length, decreased production of photosynthetic pigments, and accumulation of DNA damage) on early seedling development, whereas its administration under dark/light conditions (complete dark conditions for 5 days followed by exposure to long-day photoperiod for 5 days) bypasses some of the adverse effects. Genotoxic stress impairs plant development. To circumvent DNA damage, plants activate DNA repair pathways in concert with chromatin dynamics. These are essential during seed germination and seedling establishment, and may be influenced by photoperiod variations. To assess this interplay, an experimental design was developed in Petunia hybrida, a relevant horticultural crop and model species. Seeds were treated with different doses of sodium butyrate (NaB, 1 mM and 5 mM) as a stress agent applied under different light/dark conditions throughout a time period of 10 days. Phenotypic (germination percentage and speed, seedling length, and photosynthetic pigments) and molecular (DNA damage and gene expression profiles) analyses were performed to monitor the response to the imposed conditions. Seed germination was not affected by the treatments. Seedling development was hampered by increasing NaB concentrations applied under a long-day photoperiod (L) as reflected by the decreased seedling length accompanied by increased DNA damage. When seedlings were grown under dark conditions for 5 days and then exposed to long-day photoperiod for the remaining 5 days (D/L), the damaging effects of NaB were circumvented. NaB exposure under L conditions resulted in enhanced expression of HAT/HDAC (HISTONE ACETYLTRANSFERASES/HISTONE DEACTEYLASES) genes along with repression of genes involved in DNA repair. Differently, under D/L conditions, the expression of DNA repair genes was increased by NaB treatment and this was associated with lower levels of DNA damage. The observed DNA damage and gene expression profiles suggest the involvement of chromatin modification- and DNA repair-associated pathways in response to NaB and dark/light exposure during seedling development.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Corrado L'Andolina
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Maria Elisa Sabatini
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
- Viral Control of Cellular Pathways and Biology of Tumorigenesis Unit, European Institute of Oncology (IFOM-IEO), via Adamello 16, 20139, Milano, Italy
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química E Biológica António Xavier (ITQB-NOVA), Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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McKeown P, Spillane C. An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena. Methods Mol Biol 2020; 2093:3-13. [PMID: 32088885 DOI: 10.1007/978-1-0716-0179-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological phenomena defined as having an "epigenetic" component (according to various definitions) have been extensively studied in plant systems and illuminated many mechanisms by which gene expression is regulated and patterns of expression inherited through cell divisions. This second volume of Plant Epigenetics and Epigenomics: Methods in Molecular Biology builds on the work of its predecessor to describe cutting-edge tools for plant epigenetic and epigenomic research, and embrace crop and forestry species as well as natural populations and further insights from model species. In this chapter, the historical background to plant epigenetic and epigenomic research is summarized, and key considerations for the interpretation of current data are outlined.
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Affiliation(s)
- Peter McKeown
- Plant and Agribiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland.
| | - Charles Spillane
- Plant and Agribiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland
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39
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Lochmanová G, Ihnatová I, Kuchaříková H, Brabencová S, Zachová D, Fajkus J, Zdráhal Z, Fojtová M. Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications. Int J Mol Sci 2019; 20:ijms20205093. [PMID: 31615119 PMCID: PMC6829310 DOI: 10.3390/ijms20205093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/02/2023] Open
Abstract
A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels.
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Affiliation(s)
- Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Ivana Ihnatová
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
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40
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Sáez-Vásquez J, Delseny M. Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors. THE PLANT CELL 2019; 31:1945-1967. [PMID: 31239391 PMCID: PMC6751116 DOI: 10.1105/tpc.18.00874] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/28/2019] [Accepted: 06/25/2019] [Indexed: 05/11/2023]
Abstract
The transcription of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly of mature rRNA with ribosomal proteins are the linchpins of ribosome biogenesis. In yeast (Saccharomyces cerevisiae) and animal cells, hundreds of pre-rRNA processing factors have been identified and their involvement in ribosome assembly determined. These studies, together with structural analyses, have yielded comprehensive models of the pre-40S and pre-60S ribosome subunits as well as the largest cotranscriptionally assembled preribosome particle: the 90S/small subunit processome. Here, we present the current knowledge of the functional organization of 45S rDNA, pre-rRNA transcription, rRNA processing activities, and ribosome assembly factors in plants, focusing on data from Arabidopsis (Arabidopsis thaliana). Based on yeast and mammalian cell studies, we describe the ribonucleoprotein complexes and RNA-associated activities and discuss how they might specifically affect the production of 40S and 60S subunits. Finally, we review recent findings concerning pre-rRNA processing pathways and a novel mechanism involved in a ribosome stress response in plants.
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Affiliation(s)
- Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Michel Delseny
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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Nelson JO, Watase GJ, Warsinger-Pepe N, Yamashita YM. Mechanisms of rDNA Copy Number Maintenance. Trends Genet 2019; 35:734-742. [PMID: 31395390 DOI: 10.1016/j.tig.2019.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/28/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022]
Abstract
rDNA, the genes encoding the RNA components of ribosomes (rRNA), are highly repetitive in all eukaryotic genomes, containing 100s to 1000s of copies, to meet the demand for ribosome biogenesis. rDNA genes are arranged in large stretches of tandem repeats, forming loci that are highly susceptible to copy loss due to their repetitiveness and active transcription throughout the cell cycle. Despite this inherent instability, rDNA copy number is generally maintained within a particular range in each species, pointing to the presence of mechanisms that maintain rDNA copy number in a homeostatic range. In this review, we summarize the current understanding of these maintenance mechanisms and how they sustain rDNA copy number throughout populations.
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Affiliation(s)
- Jonathan O Nelson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - George J Watase
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Natalie Warsinger-Pepe
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Yukiko M Yamashita
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
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42
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Ha S, Zhou H, Gautam M, Song Y, Wang C. Reduced ribosomal RNA expression and unchanged ribosomal DNA promoter methylation in oral squamous cell carcinoma. Mol Genet Genomic Med 2019; 7:e00783. [PMID: 31169368 PMCID: PMC6625366 DOI: 10.1002/mgg3.783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/07/2019] [Accepted: 05/17/2019] [Indexed: 12/31/2022] Open
Abstract
Background Ribosomal RNA (rRNA) consists of four non‐coding RNAs, the 28S, 5.8S, 18S, and 5S rRNA. Abnormal expression of rRNA has been found in multiple tumors, and the methylation of rDNA promoter may affect rRNA expression as an epigenetic regulatory mechanism. Oral squamous cell carcinoma (OSCC) is a kind of aggressive tumors which occurs in multiple sites in oral cavity. rRNA expression and the methylation of rDNA promoter in modulating rRNA expression in OSCC maintain unclear. This study aims to investigate the rRNA expression, the methylation status within rDNA promoter, and the underlying mechanism of methylation in regulating rRNA expression in OSCC. Methods Twelve primary OSCC and matched normal tissue samples were collected from patients with OSCC. Quantitative real‐time PCR was used to evaluate the rRNA level. HpaII/MspI digestion and bisulfite sequencing were used to investigate the methylation status of rDNA promoter. Results Ribosomal RNA levels were suppressed in OSCC as compared with matched normal tissues. HpaII/MspI digestion and bisulfite sequencing showed no significant differences for the methylation of rDNA promoter between the tumor and matched normal tissues. Conclusion The methylation in rDNA promoter could not explain for the suppressed rRNA expression in OSCC tissues.
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Affiliation(s)
- Shanshan Ha
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mayank Gautam
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaling Song
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Changning Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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Abstract
Circadian rhythms in transcription ultimately result in oscillations of key biological processes. Understanding how transcriptional rhythms are generated in plants provides an opportunity for fine-tuning growth, development, and responses to the environment. Here, we present a succinct description of the plant circadian clock, briefly reviewing a number of recent studies but mostly emphasizing the components and mechanisms connecting chromatin remodeling with transcriptional regulation by the clock. The possibility that intergenomic interactions govern hybrid vigor through epigenetic changes at clock loci and the function of epialleles controlling clock output traits during crop domestication are also discussed.
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Affiliation(s)
- Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,Consejo Superior de Investigaciones Científicas, 08028, Barcelona, Spain.
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44
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Borowska-Zuchowska N, Robaszkiewicz E, Wolny E, Betekhtin A, Hasterok R. Ribosomal DNA loci derived from Brachypodium stacei are switched off for major parts of the life cycle of Brachypodium hybridum. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:805-815. [PMID: 30481334 PMCID: PMC6363085 DOI: 10.1093/jxb/ery425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/21/2018] [Indexed: 05/15/2023]
Abstract
Nucleolar dominance is an epigenetic phenomenon that occurs in some plant and animal allopolyploids and hybrids, whereby only one ancestral set of 35S rRNA genes retains the ability to form the nucleolus while the rDNA loci derived from the other progenitor are transcriptionally silenced. There is substantial evidence that nucleolar dominance is regulated developmentally. This study focuses upon the establishment and/or maintenance of nucleolar dominance during different stages of development in the model grass allotetraploid Brachypodium hybridum. Fluorescence in situ hybridization with a 25S rDNA probe to cells in three-dimensional cytogenetic preparations showed that nucleolar dominance is present not only in root meristematic and differentiated cells of this species, but also in male meiocytes at prophase I, tetrads of microspores, and different embryonic tissues. The inactive state of Brachypodium stacei-originated rDNA loci was confirmed by silver staining. Only B. distachyon-derived 35S rDNA loci formed nucleoli in the aforementioned tissues, whereas B. stacei-like loci remained highly condensed and thus transcriptionally suppressed. The establishment of nucleolar dominance during earlier stages of B. hybridum embryo development cannot be ruled out. However, we propose that gradual pseudogenization of B. stacei-like loci in the evolution of the allotetraploid seems to be more likely.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- Correspondence:
| | - Ewa Robaszkiewicz
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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45
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Cao L, Qin Q, Xiao Q, Yin H, Wen J, Liu Q, Huang X, Huo Y, Tao M, Zhang C, Luo K, Liu S. Nucleolar Dominance in a Tetraploidy Hybrid Lineage Derived From Carassius auratus red var. () × Megalobrama amblycephala (). Front Genet 2018; 9:386. [PMID: 30319686 PMCID: PMC6166360 DOI: 10.3389/fgene.2018.00386] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/27/2018] [Indexed: 01/09/2023] Open
Abstract
Nucleolar dominance is related to the expression of 45S rRNA genes inherited from one progenitor due to the silencing of the other progenitor’s rRNA genes. To investigate nucleolar dominance associated with tetraploidization, we analyzed the changes regarding the genetic traits and expression of 45S rRNA genes in tetraploidy hybrid lineage including F1 allotetraploids (4n = 148) and F2 autotetraploids (4n = 200) derived from the distant hybridization of Carassius auratus red var. (2n = 100) () ×Megalobrama amblycephala (2n = 48) (). Results showed that nucleolar dominance from the females was established in F1 hybrids and it was inherited in F2 hybrids, suggesting that tetraploidization can lead to rapid establishment of nucleolar dominance in the hybrid origin’s tetraploid lineage. These results extend the knowledge of nucleolar dominance in polyploidy hybrid animals, which are of significance for the evolution of hybrids in vertebrates.
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Affiliation(s)
- Liu Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - QinBo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qiong Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - HongTing Yin
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jin Wen
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - QiWen Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - YangYang Huo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - ShaoJun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China.,College of Life Sciences, Hunan Normal University, Changsha, China
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Abstract
Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools has made it possible to conduct genetic mapping and population genetic studies to unravel the molecular underpinnings of domestication and crop evolution in diverse crop species. We propose three future avenues for the study of crop evolution: establishment of high-quality reference genomes for crops and their wild relatives; genomic characterization of germplasm collections; and the adoption of novel methodologies such as archaeogenetics, epigenomics, and genome editing.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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47
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Wang B, Yang X, Wang Y, Xie Y, Zhou X. Tomato Yellow Leaf Curl Virus V2 Interacts with Host Histone Deacetylase 6 To Suppress Methylation-Mediated Transcriptional Gene Silencing in Plants. J Virol 2018; 92:e00036-18. [PMID: 29950418 PMCID: PMC6146709 DOI: 10.1128/jvi.00036-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/22/2018] [Indexed: 12/12/2022] Open
Abstract
Cytosine DNA methylation is a conserved epigenetic silencing mechanism that defends against biotic stresses such as geminivirus infection. As a countermeasure, geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing (TGS). Previous studies showed that V2 protein of Tomato yellow leaf curl virus (TYLCV) functions as a TGS suppressor. However, how V2 mediates TGS suppression remains unknown. Here we show that V2 interacts directly with a Nicotiana benthamiana histone deacetylase 6 (NbHDA6), a homolog of Arabidopsis HDA6 (AtHDA6), known to be involved in gene silencing in cooperation with methyltransferase 1 (MET1). NbHDA6 genetically complemented a late-flowering phenotype and restored histone deacetylation of an AtHDA6 mutant. Furthermore, our investigation showed that NbHDA6 displayed histone deacetylase enzymatic activity, which was not inhibited by V2. Genetic analysis revealed that silencing of NbHDA6 expression resulted in enhanced susceptibility to TYLCV infection. In addition, methylation-sensitive PCR and bisulfite sequencing analysis showed that silencing of NbHDA6 expression caused reduced DNA methylation of the viral genome in infected plants. HDA6 was previously shown to recruit and physically interact with MET1 to function in gene silencing. Using competitive pulldown and coimmunoprecipitation assays, we demonstrated that V2 did not interact but competed with NbMET1 for direct binding to NbHDA6. These findings suggest that V2 interacts with host HDA6 and interferes with the recruitment of MET1 by HDA6, resulting in decreased methylation of the viral DNA genome by TGS with a concomitant increase in host susceptibility to TYLCV infection.IMPORTANCE Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses. In turn, geminiviruses encode proteins that inhibit methylation by TGS. Previous studies showed that TYLCV V2 can efficiently suppress TGS, but the mechanism remains unknown. We showed that V2 interacted with NbHDA6 but did not inhibit its enzymatic activity. As HDA6 is known to be involved in gene silencing in cooperation with MET1, we explored the relationship between V2, NbMET1, and NbHDA6. Our investigation showed that V2 did not interact but competed with NbMET1 for direct binding to NbHDA6. To our knowledge, this is the first report that viral proteins inhibit TGS by interacting with histone deacetylase but not by blocking the methyl cycle. This work provides an additional mechanism for TGS suppression by geminiviruses.
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Affiliation(s)
- Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Nomaguchi T, Maeda Y, Yoshino T, Asahi T, Tirichine L, Bowler C, Tanaka T. Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris. BMC Genomics 2018; 19:330. [PMID: 29728068 PMCID: PMC5935921 DOI: 10.1186/s12864-018-4691-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/17/2018] [Indexed: 11/27/2022] Open
Abstract
Background Allopolyploidy is a genomic structure wherein two or more sets of chromosomes derived from divergent parental species coexist within an organism. It is a prevalent genomic configuration in plants, as an important source of genetic variation, and also frequently confers environmental adaptability and increased crop productivity. We previously reported the oleaginous marine diatom Fistulifera solaris JPCC DA0580 to be a promising host for biofuel production and that its genome is allopolyploid, which had never previously been reported in eukaryotic microalgae. However, the study of allopolyploidy in F. solaris was hindered by the difficulty in classifying the homoeologous genes based on their progenitor origins, owing to the shortage of diatom genomic references. Results In this study, the allopolyploid genome of F. solaris was tentatively classified into two pseudo-parental subgenomes using sequence analysis based on GC content and codon frequency in each homoeologous gene pair. This approach clearly separated the genome into two distinct fractions, subgenome Fso_h and Fso_l, which also showed the potency of codon usage analysis to differentiate the allopolyploid subgenome. Subsequent homoeolog expression bias analysis revealed that, although both subgenomes appear to contribute to global transcription, there were subgenomic preferences in approximately 61% of homoeologous gene pairs, and the majority of these genes showed continuous bias towards a specific subgenome during lipid accumulation. Additional promoter analysis indicated the possibility of promoter motifs involved in biased transcription of homoeologous genes. Among these subgenomic preferences, genes involved in lipid metabolic pathways showed interesting patterns in that biosynthetic and degradative pathways showed opposite subgenomic preferences, suggesting the possibility that the oleaginous characteristics of F. solaris derived from one of its progenitors. Conclusions We report the detailed genomic structure and expression patterns in the allopolyploid eukaryotic microalga F. solaris. The allele-specific patterns reported may contribute to the oleaginous characteristics of F. solaris and also suggest the robust oleaginous characteristics of one of its progenitors. Our data reveal novel aspects of allopolyploidy in a diatom that is not only important for evolutionary studies but may also be advantageous for biofuel production in microalgae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4691-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tatsuhiro Nomaguchi
- Department of Advanced Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Toru Asahi
- Department of Advanced Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Leila Tirichine
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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49
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Ding M, Chen ZJ. Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:37-48. [PMID: 29502038 PMCID: PMC6058195 DOI: 10.1016/j.pbi.2018.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 05/19/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.
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Affiliation(s)
- Mingquan Ding
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Departments of Molecular Biosciences and Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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50
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Lu KL, Nelson JO, Watase GJ, Warsinger-Pepe N, Yamashita YM. Transgenerational dynamics of rDNA copy number in Drosophila male germline stem cells. eLife 2018; 7:32421. [PMID: 29436367 PMCID: PMC5811208 DOI: 10.7554/elife.32421] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/19/2018] [Indexed: 02/02/2023] Open
Abstract
rDNA loci, composed of hundreds of tandemly duplicated arrays of rRNA genes, are known to be among the most unstable genetic elements due to their repetitive nature. rDNA instability underlies aging (replicative senescence) in yeast cells, however, its contribution to the aging of multicellular organisms is poorly understood. In this study, we investigate the dynamics of rDNA loci during aging in the Drosophila male germline stem cell (GSC) lineage, and show that rDNA copy number decreases during aging. Our study further reveals that this age-dependent decrease in rDNA copy number is heritable from generation to generation, yet GSCs in young animals that inherited reduced rDNA copy number are capable of recovering normal rDNA copy number. Based on these findings, we propose that rDNA loci are dynamic genetic elements, where rDNA copy number changes dynamically yet is maintained through a recovery mechanism in the germline.
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Affiliation(s)
- Kevin L Lu
- Life Sciences Institute, University of Michigan, Ann Arbor, United States.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, United States.,Medical Scientist Training Program, University of Michigan, Ann Arbor, United States
| | - Jonathan O Nelson
- Life Sciences Institute, University of Michigan, Ann Arbor, United States.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, United States
| | - George J Watase
- Life Sciences Institute, University of Michigan, Ann Arbor, United States.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, United States
| | - Natalie Warsinger-Pepe
- Life Sciences Institute, University of Michigan, Ann Arbor, United States.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, United States
| | - Yukiko M Yamashita
- Life Sciences Institute, University of Michigan, Ann Arbor, United States.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, United States.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, United States.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, United States
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